Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-11-10T21:53:05ZEcoinformatics Redmine
Redmine Bug #5237 (Resolved): Downloading kars on os X 10.6 locks Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/52372010-11-10T21:53:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you search for and attempt to download a remote KAR when on a mac with 10.6, Kepler freezes forever. This doesn't happen on 10.5, or other linux or windows.</p> Bug #5230 (Resolved): saving workflow that has instances of user created class to a KAR gives errorshttps://projects.ecoinformatics.org/ecoinfo/issues/52302010-10-28T18:45:31ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>User reports the following:</p>
<p>In the past year I have built many workflows as part of an on-going project... In several of these workflows I have converted a kar to a class, and then used instances of that class throughout the workflow. When I try to save this type of workflow to a kar I get errors indicating that the class cannot be found. (interestingly, there is no trouble with saving, opening, and closing these workflows as .xmls... as long as I don't convert them to kars).</p>
<p>I'm attaching two versions of the same simple workflow: an xml and a kar, both of which display the result of an instance of an "expression class" (the expression actor converted to a class), as well as the error which ensues from attempting to open the kar. Note that we do not save our workflows to the KeplerData directory.</p> Bug #5229 (Resolved): Poor component search performancehttps://projects.ecoinformatics.org/ecoinfo/issues/52292010-10-28T17:15:31ZJing Taotao@nceas.ucsb.edu
<p>Here is email from Matt:</p>
<p>Hi Jing,</p>
<p>Another thing about Kepler -- I noticed that that the search for remote components is 1) painfully slow, 2) has not search status indicator, and 3) seems to freeze up the app while it is searching. These things combined make for a painful user experience.</p>
<p>Matt also mentioned we should double check if every search is doing a Metacat read on every matching kars. If it does, we may change this to a single hit on metacat.</p> Bug #5225 (Resolved): problems loading & saving KARs when disconnectedhttps://projects.ecoinformatics.org/ecoinfo/issues/52252010-10-26T18:22:05ZDaniel Crawldanielcrawl@gmail.com
<p>I can't open a workflow KAR without a network connection. Here's the exception:</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:530)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:242)<br /> at org.kepler.kar.KARFile.open(KARFile.java:968)<br /> at org.kepler.kar.KARFile.openKARContents(KARFile.java:736)<br /> at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:182)<br /> at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:160)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6348)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6113)<br /> at java.awt.Container.processEvent(Container.java:2085)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4714)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): ptolemy.eecs.berkeley.edu<br /> at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:260)<br /> at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)<br /> at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)<br /> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)<br /> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:518)<br /> ... 33 more</p>
<p>I also get the following exception when I save a KAR, but the KAR appears to be created:</p>
<p>done writing KAR file to /Users/crawl/KeplerData/workflows/MyWorkflows/01-SimpleAddition.kar<br />java.net.UnknownHostException: ptolemy.eecs.berkeley.edu<br /> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)<br /> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:432)<br /> at java.net.Socket.connect(Socket.java:529)<br /> at java.net.Socket.connect(Socket.java:478)<br /> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)<br /> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)<br /> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)<br /> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)<br /> at sun.net.www.http.HttpClient.New(HttpClient.java:306)<br /> at sun.net.www.http.HttpClient.New(HttpClient.java:323)<br /> at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:860)<br /> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:801)<br /> at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:726)<br /> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1049)<br /> at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)<br /> at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)<br /> at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)<br /> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)<br /> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br /> at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br /> at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)<br /> at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:104)<br /> at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorCacheObject.java:143)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:212)<br /> at org.kepler.kar.KARFile.cache(KARFile.java:920)<br /> at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:633)<br /> at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:185)<br /> at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:429)<br /> at org.kepler.gui.kar.SaveArchiveAction.actionPerformed(SaveArchiveAction.java:89)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6348)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6113)<br /> at java.awt.Container.processEvent(Container.java:2085)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4714)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Error parsing Actor KAR DOM "<?xml version="1.0"?><br /><!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br /> "http://ptolemy.e...": ptolemy.eecs.berkeley.edu<br />MC 18:57:45,405: [WARN]: KAREntry has no lsid: null [org.kepler.objectmanager.cache.CacheManager]</p> Bug #5203 (Resolved): Kepler wont starthttps://projects.ecoinformatics.org/ecoinfo/issues/52032010-10-18T17:01:17ZDavid LeBauerdlebauer@gmail.com
<p>I usually start Kepler with the command ./Kepler-2.0/kepler.sh</p>
<p>Today, this gives me the error below. Reinstalling Kepler and Java do not help.</p>
<p>Here is the output:</p>
<p>dlebauer@dlebauer-desktop:~$ ./Kepler-2.0/kepler.sh <br /> [null] Exception in thread "main" java.lang.NoClassDefFoundError: org/kepler/Kepler<br /> [null] Caused by: java.lang.ClassNotFoundException: org.kepler.Kepler<br /> [null] at java.net.URLClassLoader$1.run(URLClassLoader.java:202)<br /> [null] at java.security.AccessController.doPrivileged(Native Method)<br /> [null] at java.net.URLClassLoader.findClass(URLClassLoader.java:190)<br /> [null] at java.lang.ClassLoader.loadClass(ClassLoader.java:307)<br /> [null] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)<br /> [null] at java.lang.ClassLoader.loadClass(ClassLoader.java:248)<br /> [null] Could not find the main class: org.kepler.Kepler. Program will exit.<br />Exception in thread "main" Java returned: 1<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br />Caused by: Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> ... 1 more<br />--- Nested Exception ---<br />Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)</p> Bug #5168 (Resolved): 'ant change-to' fails at r25610https://projects.ecoinformatics.org/ecoinfo/issues/51682010-09-01T16:49:50ZDaniel Crawldanielcrawl@gmail.com
<ol>
<li>ant change-to -Dsuite=kepler<br />Buildfile: build.xml</li>
</ol>
<p>change-to:<br />[change-to] Retrieving modules....<br />[change-to] <br />[change-to] The module kepler already exists.<br />[change-to] The module outreach already exists.<br />[change-to] The module apple-extensions already exists.<br />[change-to] The module r already exists.<br />[change-to] The module loader already exists.<br />[change-to] The module actors already exists.<br />[change-to] The module directors already exists.<br />[change-to] The module opendap already exists.<br />[change-to] The module dataturbine already exists.<br />[change-to] The module ecogrid already exists.<br />[change-to] The module authentication-gui already exists.<br />[change-to] The module module-manager-gui already exists.<br />[change-to] The module gui already exists.<br />[change-to] The module authentication already exists.<br />[change-to] The module repository already exists.<br />[change-to] The module job already exists.<br />[change-to] The module io already exists.<br />[change-to] The module ssh already exists.<br />[change-to] The module data-handling already exists.<br />[change-to] The module sms already exists.<br />[change-to] The module component-library already exists.<br />[change-to] The module util already exists.<br />[change-to] The module event-state already exists.<br />[change-to] The module core already exists.<br />[change-to] The module common already exists.<br />[change-to] The module module-manager already exists.<br />[change-to] The module configuration-manager already exists.<br />[change-to] The module kepler-tasks already exists.<br />[change-to] The module ptolemy already exists.<br />[change-to] <br />[change-to] Changing the value of modules.txt<br />[change-to] java.io.FileNotFoundException: /Users/crawl/KeplerData/kepler.modules/build-area/current-suite.txt (No such file or directory)<br />[change-to] at java.io.FileOutputStream.open(Native Method)<br />[change-to] at java.io.FileOutputStream.<init>(FileOutputStream.java:179)<br />[change-to] at java.io.FileOutputStream.<init>(FileOutputStream.java:131)<br />[change-to] at java.io.FileWriter.<init>(FileWriter.java:73)<br />[change-to] at org.kepler.build.modules.CurrentSuiteTxt.setName(CurrentSuiteTxt.java:68)<br />[change-to] at org.kepler.build.ChangeTo.run(ChangeTo.java:137)<br />[change-to] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br />[change-to] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)<br />[change-to] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)<br />[change-to] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br />[change-to] at java.lang.reflect.Method.invoke(Method.java:597)<br />[change-to] at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)<br />[change-to] at org.apache.tools.ant.Task.perform(Task.java:348)<br />[change-to] at org.apache.tools.ant.Target.execute(Target.java:357)<br />[change-to] at org.apache.tools.ant.Target.performTasks(Target.java:385)<br />[change-to] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)<br />[change-to] at org.apache.tools.ant.Project.executeTarget(Project.java:1306)<br />[change-to] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)<br />[change-to] at org.apache.tools.ant.Project.executeTargets(Project.java:1189)<br />[change-to] at org.apache.tools.ant.Main.runBuild(Main.java:758)<br />[change-to] at org.apache.tools.ant.Main.startAnt(Main.java:217)<br />[change-to] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)<br />[change-to] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)</p>
<p>BUILD FAILED<br />java.lang.NullPointerException<br /> at org.kepler.build.modules.CurrentSuiteTxt.setName(CurrentSuiteTxt.java:74)<br /> at org.kepler.build.ChangeTo.run(ChangeTo.java:137)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)<br /> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)<br /> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br /> at java.lang.reflect.Method.invoke(Method.java:597)<br /> at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)<br /> at org.apache.tools.ant.Task.perform(Task.java:348)<br /> at org.apache.tools.ant.Target.execute(Target.java:357)<br /> at org.apache.tools.ant.Target.performTasks(Target.java:385)<br /> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)<br /> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)<br /> at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)<br /> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)<br /> at org.apache.tools.ant.Main.runBuild(Main.java:758)<br /> at org.apache.tools.ant.Main.startAnt(Main.java:217)<br /> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)<br /> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)</p>
<p>Total time: 0 seconds</p> Bug #5115 (Resolved): enable system properties setting by updating kepler.sh or kepler.bathttps://projects.ecoinformatics.org/ecoinfo/issues/51152010-07-30T19:35:42Zjianwu jianwujianwu@sdsc.edu
<p>Originally reported by Chris Weed by asking how to launch kepler 2.0 with proxy settings(<a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-July/002269.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-July/002269.html</a>)</p>
<p>After digging a while, I found that all property setting by updating kepler.sh or kepler.bat can not take affect. From org.kepler.build.Run class, you can see it started another JVM to start org.kepler.Kepler class without accepting properties from org.kepler.build.runner.Kepler class. I think it is why the properties Chris set works for org.kepler.Kepler, but not org.kepler.build.runner.Kepler.</p> Bug #5098 (Resolved): Save Archive (KAR)... will have exception when internet is not accessible.https://projects.ecoinformatics.org/ecoinfo/issues/50982010-07-19T22:30:21Zjianwu jianwujianwu@sdsc.edu
<p>Found by Chris Weed, I can reproduce it.</p>
<p>It happens when I right-click the actor, choose 'Save Archive (KAR)...' and try to save its kar file, no matter whether I choose 'Add Semantic Types' or not. </p>
<pre><code>[null] done writing KAR file to C:\Users\jianwu\KeplerData\workflows\MyWorkflows\ttt.kar<br /> [null] java.net.UnknownHostException: ptolemy.eecs.berkeley.edu<br /> [null] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)<br /> [null] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)<br /> [null] at java.net.Socket.connect(Socket.java:529)<br /> [null] at java.net.Socket.connect(Socket.java:478)<br /> [null] at sun.net.NetworkClient.doConnect(NetworkClient.java:163)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)<br /> [null] at sun.net.www.http.HttpClient.&lt;init&gt;(HttpClient.java:233)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:306)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:323)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:860)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:801)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:726)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1049)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)<br /> [null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:101)<br /> [null] at org.kepler.objectmanager.cache.ActorCacheObject.&lt;init&gt;(ActorCacheObject.java:141)<br /> [null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:169)<br /> [null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br /> [null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br /> [null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br /> [null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:344)<br /> [null] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> [null] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> [null] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [null] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [null] at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> [null] at java.awt.Component.processMouseEvent(Component.java:6263)<br /> [null] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> [null] at java.awt.Component.processEvent(Component.java:6028)<br /> [null] at java.awt.Container.processEvent(Container.java:2041)<br /> [null] at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> [null] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> [null] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> [null] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> [null] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br /> [null] &lt;!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br /> [null] "http://ptolemy.e...": ptolemy.eecs.berkeley.edu<br /> [null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br /> KAREntry has no lsid: null</code></pre>
<pre><code>It has similar exception when proxy is needed to access internet. The problem Chris found is as follows.</code></pre>
<p>I think the problem I am having is that it is trying to validate the XML against<br /><a class="external" href="http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd">http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd</a>, and my proxy<br />is probably in the way. Although I set the proxy in the kepler.bat file on the<br />command-line. I am not sure why it isn't going through.<br />Chris</p>
<p>[null] java.net.ConnectException: Connection timed out: connect<br />[null] at java.net.PlainSocketImpl.socketConnect(Native Method)<br />[null] at java.net.PlainSocketImpl.doConnect(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connectToAddress(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connect(Unknown Source)<br />[null] at java.net.SocksSocketImpl.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at sun.net.NetworkClient.doConnect(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.<init>(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(<br />Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unkn<br />own Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown S<br />ource)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown S<br />ource)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknow<br />n Source)<br />[null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unkno<br />wn Source)<br />[null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.d<br />ispatch(Unknown Source)<br />[null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDoc<br />ument(Unknown Source)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br />[null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br />[null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Sour<br />ce)<br />[null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(<br />KeplerMetadataExtractor.java:101)<br />[null] at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorC<br />acheObject.java:141)<br />[null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(Ac<br />torMetadataKAREntryHandler.java:169)<br />[null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br />[null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br />[null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br />[null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(Export<br />ArchiveAction.java:344)<br />[null] at javax.swing.AbstractButton.fireActionPerformed(Unknown Source<br />)<br />[null] at javax.swing.AbstractButton$Handler.actionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.setPressed(Unknown Source)<br />[null] at javax.swing.AbstractButton.doClick(Unknown Source)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source<br />)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(<br />Unknown Source)<br />[null] at java.awt.Component.processMouseEvent(Unknown Source)<br />[null] at javax.swing.JComponent.processMouseEvent(Unknown Source)<br />[null] at java.awt.Component.processEvent(Unknown Source)<br />[null] at java.awt.Container.processEvent(Unknown Source)<br />[null] at java.awt.Component.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Sou<br />rce)<br />[null] at java.awt.LightweightDispatcher.processMouseEvent(Unknown Sour<br />ce)<br />[null] at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Window.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventQueue.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Sour<br />ce)<br />[null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.run(Unknown Source)<br />[null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br />[null] <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br />[null] "http://ptolemy.e...": Connection timed out: connect<br />[null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br />KAREntry has no lsid: null</p> Bug #5092 (Resolved): 2.0 user manual has no table of contentshttps://projects.ecoinformatics.org/ecoinfo/issues/50922010-07-14T16:37:49ZDaniel Crawldanielcrawl@gmail.com
<p>The Kepler 2.0 User Manual has no table of contents or index, making it somewhat difficult to find things in the 386 page document.</p>
<p><a class="external" href="https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/2.0/UserManual.pdf">https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/2.0/UserManual.pdf</a></p> Bug #5051 (Resolved): Semantically annotate during Save Archive a workflow with remote data set E...https://projects.ecoinformatics.org/ecoinfo/issues/50512010-06-16T20:48:37ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you search for a remote data set, drag it out to canvas, then Save Archive, and then Semantically Annotate the workflow, you'll get a NameDuplicationException and the window will dispose, and the kar is failed to be saved properly (and thus a new window with the saved workflow does not open (as is usually the case)).</p>
<p>I'm seeing this in RC5, 2.0 branch, and trunk.</p>
<p>Replicate:<br />Start Kepler, change to Data tab<br />Search Data for: aphid<br />drag out the 2nd dataset (Sedgwick Reserve Aphid Population Growth Rate Experiment)<br />File => Save Archive<br />Name workflow myWorkflow<br />Click yes to semantically annotate<br />Select a category, like Local Input, and move it to Selected Categories<br />Click ok, Click Save, and the window will dispose with the NameDuplicationError</p> Bug #5029 (Resolved): Parameter changes can be committed without clicking the commit buttonhttps://projects.ecoinformatics.org/ecoinfo/issues/50292010-05-25T18:25:09ZSean Riddleswriddle@gmail.com
<p>1) Double-click on an actor and change a parameter.<br />2) Click the add button to trigger the "add parameter" dialog<br />3) Click Cancel</p>
<p>At this point, you're dumped back to the canvas, and your alteration to the parameter of the actor has been committed. Seems like the preferred behavior is either dumping the user back to the canvas with all changes rolled back, or (even better) just return the user to the normal parameter change dialog after they're done with the add parameter dialog.</p>
<p>I've managed to produce this on the RC3 installer on Windows XP, and on the Kepler trunk on a Mac.</p> Bug #5024 (Resolved): Uninstaller couldn't delete the rc3 folder on windows 7https://projects.ecoinformatics.org/ecoinfo/issues/50242010-05-20T22:01:15ZJing Taotao@nceas.ucsb.edu
<p>Uninstaller couldn't remove the rc3 folder in Program File on Windows 7 (Vista). But it can remove desktop icon and kepler menu item on "Start" menu.</p>
<p>RC2 uninstaller has the same issue.</p>
<p>Morpho had the same problem. But after upgrading IzPack to 4.3.1, the bug was fixed.</p> Bug #5023 (Resolved): The desktop icon of rc3 is a blank page on windows vistahttps://projects.ecoinformatics.org/ecoinfo/issues/50232010-05-20T21:00:20ZJing Taotao@nceas.ucsb.edu
<p>The icon is a blank page on windows. It was a issue on rc2 as well.</p> Bug #5022 (Resolved): 2.0-RC3 Windows installer creates Kepler 2.0-RC2 start menu choice, not Kep...https://projects.ecoinformatics.org/ecoinfo/issues/50222010-05-20T19:52:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>With the Kepler-2.0-RC3 Windows installer, the shortcut in Start->All Programs<br />->Kepler is Kepler 2.0-RC2, not Kepler-2.0-RC3.</p>
<p>Also, the icon for "Kepler 2.0-RC2" is missing, I get a default<br />icon, not the Kepler Icon.</p> Bug #5021 (Resolved): release date is wrong in installer readmehttps://projects.ecoinformatics.org/ecoinfo/issues/50212010-05-20T18:42:15ZChad Berkleyberkley@nceas.ucsb.edu
<p>change the date to the actual release date. it's set as may 12 right now.</p>